STAR 2.5.4a 2018/01/23

Implemented read group ID output as the last column of the Chimeric.out.junction file.
Implemented --readFilesPrefix option for specifying prefix (e.g. directory path) for the file names in --readFilesIn .
Implemented standard SAM attribute "MC" to output the mate's CIGAR. Add MC to the list of attributes in the --outSAMattribute option.
Implemented the ability to input the reads from unmapped SAM/BAM file: --readFilesType SAM SE[PE] for single-end [paired-end] reads to read from the SAM file specified, as usual in --readFilesIn. For BAM files, in addition, specify --readFilesCommand samtools view -h .
Implemented --seedSplitMin option which was previously hardcoded at 12. his will allow mapping of mates shorter than 12nt.
Implemented --outFilterIntronStrands None option to switch off filtering by strand consistency of junctions.
Added new scripts extras/scripts/mergeLogFinal.awk,mergeSuperContig.awk,sjMotif.m

Fixed a bug in chimeric detection code which sometimes led to uninitialized memory access. The chimeric output may change for a very small number of reads.
Fixed a problem with --alignEndsProtrude implementation which prevented the output of alignments with protruded ends.
Fixed a bug which set non-primary bit 0x100 in the SAM FLAG for unmapped mates.
Fixed a bug in liftOver command that output an extra field in the GTF file.
Fixed a problem that can arise for very small genomes while using --alignIntronMax 1.

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